On Mon, Aug 25, 2008 at 11:00 AM, Martin Morgan <[EMAIL PROTECTED]> wrote:
> Michael Lawrence wrote:
>
>> I might be wrong here, but it might be possible to run ShortRead on R
>> 2.7.2
>> with all its dependencies (Biostrings, IRanges, ...) installed from
>> Bioconductor 2.3.
>>
>
> It won't, because ShortRead has C-level dependencies on two packages, and
> this support was not working until relatively recently in R-devel
> (r46267, Fri, 08 Aug 2008, I think).
>
But R 2.7.2 includes that fix, I think.
>
> In general I've found (though I'll admit to not being an ordinary R user)
> that the cost to switching versions is minimal, and that R-devel rarely has
> changes that fundamentally break what was previously working. If the need is
> for a package that has seen recent heavy development (ShortRead and
> Biostrings definitely fall into this category), then I'd recommend switching
> to using R-devel.
>
> Martin
>
>
>
> On Mon, Aug 25, 2008 at 9:25 AM, Patrick Aboyoun <[EMAIL PROTECTED]>
>> wrote:
>>
>> Terry,
>>> The ShortRead package is only available for the BioC 2.3 / R-devel code
>>> line. It depends on the development version of Biostrings. A number of C
>>> interfaces to Biostrings were opened up in the development version of
>>> Biostrings to allow packages like ShortRead to have a tight integration
>>> for
>>> fast string manipulation. Using biocLite("ShortRead") when running
>>> R-devel
>>> will get you up and running.
>>>
>>>
>>> Cheers,
>>> Patrick
>>>
>>>
>>>
>>> Terry Therneau wrote:
>>>
>>> I have tried to install the shortreads package, with no success.
>>>>
>>>> tmt36% R
>>>>
>>>> R version 2.7.0 (2008-04-22)
>>>> Copyright (C) 2008 The R Foundation for Statistical Computing
>>>> ISBN 3-900051-07-0
>>>>
>>>>
>>>>
>>>> biocLite('ShortRead')
>>>>>
>>>>>
>>>>> Running biocinstall version 2.1.11 with R version 2.7.0 Your version
>>>> of R
>>>> requires version 2.1 of BioConductor.
>>>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
>>>> dependencies, :
>>>> argument 'lib' is missing: using
>>>> '/home/therneau/R/x86_64-unknown-linux-gnu-library/2.7'
>>>> Warning message:
>>>> In install.packages(pkgs = pkgs, repos = repos, dependencies =
>>>> dependencies, :
>>>> package âShortReadâ is not available
>>>>
>>>> ----
>>>> The bottom line says it all.
>>>> So then I tried downloading the source, and using the standard R
>>>> install.packages call. That fails because it expects
>>>> "_Biostrings_stubs.c"
>>>> to be in the standard R include directory, which is clearly false.
>>>> I'd like to install the new material in my own library -- but it
>>>> rather
>>>> looks like bioconductor as a whole is designed to NOT work with the
>>>> usual R
>>>> install tools. Is this correct? (Bioconductor as a whole is installed
>>>> on
>>>> the system by our administrator).
>>>> Terry Therneau
>>>> (working with Solexa data)
>>>>
>>>> _______________________________________________
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>>>> [email protected]
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>>>
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>>
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>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
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